constrain-JULES-ES-1p0.Rmd

Sensitivity analysis and constraint of the parameter space of Earth System configuration of JULES.

Update of explore-JULES-ES-1p0.Rmd that uses the new packages and functions

Andy thinks there might be mileage in analysing the atmospheric growth, which is here. /home/h01/hadaw/Research/ES_PPE/Oct20

At the moment, this vignette is hampered by the fact that emulators are failing on a few of the outputs which represent change over the historical perid. The emulator is fine for predicting absolute values in the modern period.

Andy would like to see timeseries of: cVeg, cSoil and nbp, npp in GtC and GtC/yr.

# Load helper functions

knitr::opts_chunk$set(fig.path = "figs/", echo = TRUE, message = FALSE, warnings = FALSE)
# load some helper functions
source('~/brazilCSSP/code/brazil_cssp/per_pft.R') # eventually, move the relevant functions
source('explore-JULES-ES-1p0_PPE_functions.R')

# Load packages

library(RColorBrewer)
library(fields)
library(MASS)
library(DiceKriging)
library(ncdf4)
library(ncdf4.helpers)

library(foreach)

library(emtools)
library(imptools)
library(viztools)
library(julesR)

# Preliminaries
# Some pallete options
yg = brewer.pal(9, "YlGn")
ryb = brewer.pal(11, "RdYlBu")
byr = rev(ryb)
rb = brewer.pal(11, "RdBu")
br = rev(rb)
blues = brewer.pal(9, 'Blues')
cbPal <- c("#000000", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")

ysec = 60*60*24*365
years <- 1850:2013

Jules output data location

ensloc <- '/project/carbon_ppe/JULES-ES-1p0_PPE/'
ensmember <- 'P0000/'
subdir <- 'stats/'

floc <- paste0(ensloc,ensmember,subdir)
fn <- 'JULES-ES-1p0_P0000_Annual_global.nc'

# test file
nc <- nc_open(paste0(floc,fn))

# What variables are in the file? 
varlist <- nc.get.variable.list(nc)

Extract a time series of an annual, globally aggregated variable

extractTimeseries <- function(nc, variable){
    dat <- ncvar_get(nc, variable)
    out <- dat
    out
}

makeTimeseriesEnsemble <- function(variable, nens = 499, nts = 164, cn = 1850:2013){
  
  # nens is number of ensemble members
  # nts length of timeseries
  # cn is colnames()
  datmat <- matrix(NA, nrow = nens, ncol = nts)
  colnames(datmat) <- cn
  
  enslist <- paste("P", formatC(0:(nens-1), width=4, flag="0"), sep="")
  floc <- paste0(ensloc,ensmember,subdir)
  
  for(i in 1:nens){
    
    vec <- rep(NA,nts)
    
    ensmember <- enslist[i] 
    
    fn <- paste0(ensloc,ensmember,'/stats/','JULES-ES-1p0_',ensmember,'_Annual_global.nc')
 
    
    try(nc <- nc_open(paste0(fn)))
    try(dat <- extractTimeseries(nc, variable))
    
    datmat[i, ] <- dat
    nc_close(nc)
  }
  datmat
}

Test with the global sum of NPP and plot the timeseries

par(mfrow= c(2,2))

ylim = range(c(nbp_ens[,1], nbp_ens[,164]))
matplot(years, t(nbp_ens), type = 'l', lty = 'solid',ylim = ylim, col = cbPal, ylab = 'NBP sum', main = 'NBP')

ylim = range(c(npp_ens[,1], npp_ens[,164]))
matplot(years, t(npp_ens), type = 'l', lty = 'solid',ylim = ylim, col = cbPal, ylab = 'NPP sum', main = 'NPP')

ylim = range(c(cSoil_ens[,1], cSoil_ens[,164]))
matplot(years, t(cSoil_ens), type = 'l', lty = 'solid',ylim = ylim, col = cbPal, ylab = 'Soil carbon sum', main = 'Soil Carbon')

ylim = range(c(cVeg_ens[,1], cVeg_ens[,164]))
matplot(years, t(cVeg_ens), type = 'l', lty = 'solid',ylim = ylim, col = cbPal, ylab = 'Veg carbon sum', main = 'Vegetation Carbon')

Function to extract the “modern value” direct from the file (last 20 years of the timeseries)

# for each of the variables in the file, average the last 20 years as the "modern" value,
# and then place in a matrix

modernValue <- function(nc, variable, ix){
  # A basic function to read a variable and 
  # take the mean of the timeseries at locations ix
  dat <- ncvar_get(nc, variable)
  out <- mean(dat[ix])
  out
}
#144:164 is the 1993:2013
modernValue(nc = nc, variable = "npp_nlim_lnd_mean", ix = 144:164)

# apply to the test file to check it works
vec <- sapply(varlist, FUN = modernValue, nc = nc, ix = 144:164)

Loop to extract the “modern value” of a number of model outputs

# Generate ensemble numbers, mean of the last 20 years of the timeseries (1994-2013)

if (file.exists("ensemble.rdata")) {
  load("ensemble.rdata")
} else {
  
  nens = 499
  datmat <- matrix(nrow = nens, ncol = length(varlist))
  colnames(datmat) <- varlist
  
  enslist <- paste("P", formatC(0:(nens-1), width=4, flag="0"), sep="")
  floc <- paste0(ensloc,ensmember,subdir)
  
  for(i in 1:nens){
    
    vec <- rep(NA, length(varlist))
    
    ensmember <- enslist[i] 
    
    fn <- paste0(ensloc,ensmember,'/stats/','JULES-ES-1p0_',ensmember,'_Annual_global.nc')
    #print(fn)
    
    try(nc <- nc_open(paste0(fn)))
    try(vec <- sapply(varlist, FUN = modernValue, nc = nc, ix = 144:164))
    datmat[i, ] <- vec
    nc_close(nc)
  }
  
  save(nens, datmat,enslist,floc, file ="ensemble.rdata")
}

Calculate an ensemble of anomalies for all variables

For each ensemble member and each variable, calculate the change from the 20 years at the start of the run, to the twenty years at the end of the run.

tsAnomaly <- function(nc, variable, startix = 1:20, endix = 144:164){

  # A basic function to read a variable and calculate the anomaly at the end of the run
  dat <- ncvar_get(nc, variable)
  endMean <- mean(dat[endix])
  startMean <- mean(dat[startix])
  out <- endMean - startMean
  out
}

tsAnomaly(nc = nc, variable = "npp_nlim_lnd_mean")

## [1] 2.410932e-09

# Generate ensemble  mean of the last 20 years of the timeseries (1994-2013)

if (file.exists("anomaly_ensemble.rdata")) {
  load("anomaly_ensemble.rdata")
} else {
  
  nens = 499
  datmatAnom <- matrix(nrow = nens, ncol = length(varlist))
  colnames(datmatAnom) <- varlist
  
  enslist <- paste("P", formatC(0:(nens-1), width=4, flag="0"), sep="")
  floc <- paste0(ensloc,ensmember,subdir)
  
  for(i in 1:nens){
    
    vec <- rep(NA, length(varlist))
    
    ensmember <- enslist[i] 
    
    fn <- paste0(ensloc,ensmember,'/stats/','JULES-ES-1p0_',ensmember,'_Annual_global.nc')
    #print(fn)
    
    try(nc <- nc_open(paste0(fn)))
    try(vec <- sapply(varlist, FUN = tsAnomaly, nc = nc))
    datmatAnom[i, ] <- vec
    nc_close(nc)
  }
  
  save(nens, datmatAnom, enslist,floc, file ="anomaly_ensemble.rdata")
}

Probability of run failure

Could be an interesting project - logit transformation for probability of run failure? Some other ML like SVM?

Clean data sets

# Initial clean of data set, removing variables that don't change, and removing NAs (models that didn't run)

Y_nlevel0_ix <- which(is.na(datmat[,'year']))

YAnom_nlevel0_ix <- which(is.na(datmatAnom[,'year']))

# This should be true to proceed, or we'll have to start excluding the combined set.
identical(Y_nlevel0_ix, YAnom_nlevel0_ix)

## [1] TRUE

# Y is the whole data set
Y <- datmat
# Y_level0 is the 'cleaned' data set, truncated to variables that change, and removing NAs
Y_level0 <- datmat[-Y_nlevel0_ix, -c(2,30,31)]
Y_nlevel0 <- datmat[Y_nlevel0_ix, -c(2, 30, 31)]


# Y is the whole data set
YAnom <- datmatAnom
# Y.level0 is the 'cleaned' data set, truncated to variables that change, and removing NAs
YAnom_level0 <- datmatAnom[-YAnom_nlevel0_ix, -c(2,30,31)]
YAnom_nlevel0 <- datmatAnom[YAnom_nlevel0_ix, -c(2,30,31)]

# load the original design and input space, normalize to [0-1]



# Load up the data
lhs_i = read.table('~/brazilCSSP/code/brazil_cssp/analyze_u-ao732/data/ES_PPE_i/lhs_u-ao732.txt', header = TRUE)
lhs_ii = read.table('~/brazilCSSP/code/brazil_cssp/analyze_u-ao732/data/ES_PPE_ii/lhs_u-ao732a.txt', header = TRUE)

toplevel_ix = 1:499

# The raw input data is a latin hypercube
lhs = rbind(lhs_i, lhs_ii)[toplevel_ix, ]
lhs_level0 <- lhs[-Y_nlevel0_ix,]

X = normalize(lhs)
colnames(X) = colnames(lhs)

X_level0 <- X[-Y_nlevel0_ix,]
X_nlevel0 <- X[Y_nlevel0_ix,]

d = ncol(X)
# lower and higher bound on the normalised matrix for visualisation
rx = rbind(rep(0,32), rep(1,32))

Where did the model fail to run?

There are clear run failure thresholds in the parameters rootd_ft_io and lai_max, and quite strong visual indications that a_wl_io and bio_hum_cn matter.

#simple way
par(oma = c(10,10,0,0))
#par(xpd = TRUE)
pairs(X_nlevel0, 
      xlim = c(0,1), ylim = c(0,1),
      col = 'red', 
      gap = 0,
      pch = 20,
      lower.panel = NULL)

#legend('bottomright', legend = paste(1:d, colnames(lhs)), bty = 'n')
legend('left', col = 'red', pch = 20, legend = 'test')

# plot failures over everything else
#X.all <- rbind(X.level0, X.nlevel0)
#colvec <- rep('grey', nrow(X))
#colvec[(nrow(X.level0)+1):nrow(X.all)] <- 'red'
#pairs(X.all, xlim = c(0,1), ylim = c(0,1),col = colvec, gap = 0, lower.panel = NULL, pch = 20, cex = 0.5)

Build some Gaussian Process emulators

First, use mean NPP as an example. How does NPP respond to each parameter? NAs are removed, but zero values are still included.

p <- ncol(X_level0)

y_level0 <- Y_level0[,'npp_nlim_lnd_sum']

par(mfrow = c(5,7), mar = c(3,1,3,1), oma = c(1,1,5,1))
for(i in 1:p){
  plot(X_level0[,i], y_level0, xlab = '', ylab = '', main = colnames(X_level0)[i])
}
mtext('NPP', outer = TRUE, side = 3, cex = 2, line = 2)

yanom_level0 <- YAnom_level0[,'npp_nlim_lnd_sum']

par(mfrow = c(5,7), mar = c(3,1,3,1), oma = c(1,1,5,1))
for(i in 1:p){
  plot(X_level0[,i], yanom_level0, xlab = '', ylab = '', main = colnames(X_level0)[i])
}
mtext('NPP change over time', outer = TRUE, side = 3, cex = 2, line = 2)

Relationship between modern value and change since 1850.

Some outputs (e.g fLuc, fHarvest) have an almost perfect 1:1 relationship between modern value and change, some (nbp, npp, treeFrac) quite or moderately strong, and some (csoil, cveg) very weak or non-existant.

par(mfrow = c(4,7), mar = c(3,1,3,1), oma = c(4,5,1,1))

pdash <- ncol(Y_level0)

for(i in 1:pdash){
  
  y_level0 <- Y_level0[,i]
  yanom_level0 <- YAnom_level0[,i]
  
  plot(y_level0, yanom_level0, xlab = '', ylab = '', main = colnames(Y_level0)[i])
}

mtext(text = 'Modern value', side = 1, line = 2, outer = TRUE, cex = 2)
mtext(text = 'Change', side = 2, line = 2, outer = TRUE, cex = 2)

A clear threshold in the F0 parameter.

It appears that this ensemble is less “clear cut” in having an output that clearly distinguishes between “failed” (or close to it), and “not failed”.

Having said that, having an F0 over a threshold seems to kill the carbon cycle, as before. Here, we’ve set a threshold of 0.9 (on the normalised scale) for F0, and we remove members of the ensemble with a larger F0 than that when we build emulators.

par(mfrow = c(2,1))
plot(lhs$f0_io, datmat[, 'npp_nlim_lnd_sum'], main = 'Multiplication factor', xlab = 'f0_io', ylab = 'NPP sum')
plot(X_level0[,'f0_io'], Y_level0[, 'npp_nlim_lnd_sum'], xlab = 'f0_io', main = 'Normalized', ylab = 'NPP sum')
abline(v = 0.9)

Remove anything with f0 over a threshold (level 1 constraint) .

The level 1 constraint removes any input with F0 greater than 0.9 (normalised), which removes many of the zero-carbon-cycle members up front. There are 424 ensmble members remaining.

This does constraint sequentially, which may not be a good idea.

level1_ix <- which(X_level0[, 'f0_io'] < 0.9)

X_level1 <- X_level0[level1_ix, ]
Y_level1 <- Y_level0[level1_ix,]

YAnom_level1 <- YAnom_level0[level1_ix, ]

y_level1 <- Y_level1[, 'npp_nlim_lnd_sum']

em_level1 <- km(~., design = X_level1,  response = y_level1)

plot(X_level1[, 'f0_io'], Y_level1[, 'npp_nlim_lnd_sum'], xlab = 'f0_io (normalised)', ylab = 'NPP')

# Plot the regular km emulator. Doesn’t look great.

plot(em_level1)

Constrain first and then do sensitivity analysis?

The problem with doing constraint first is that you end up with a non-hypercube shaped input space (corners have been knocked off by constraint), which is not ideal. We might therefore want different sensitivity measures for pre- and post-constrained ensemble.

#sensvar needs to go into emtools with oaat_design
sensvar <- function(oaat_pred, n, d){
  # Calculate variance as a global sensitivity meansure
  out = rep(NA,d)
  for(i in 1:d){
    ix = seq(from = ((i*n) - (n-1)), to =  (i*n), by = 1)
    out[i] = var(oaat_pred$mean[ix])
  }
  out
}

twoStep_glmnet <- function(X, y, nugget=NULL, nuggetEstim=FALSE, noiseVar=NULL, seed=NULL, trace=FALSE, maxit=100,
                          REPORT=10, factr=1e7, pgtol=0.0, parinit=NULL, popsize=100){
  # Use lasso to reduce input dimension of emulator before
  # building.
  control_list = list(trace=trace, maxit=maxit, REPORT=REPORT, factr=factr, pgtol=pgtol, pop.size=popsize)
  xvars = colnames(X)
  data = data.frame(response=y, x=X)
  colnames(data) <- c("response", xvars)
  nval = length(y)
  
  # fit a lasso by cross validation
  library(glmnet)
  fit_glmnet_cv = cv.glmnet(x=X,y=y)
  
  # The labels of the retained coefficients are here
  # (retains intercept at index zero)
  coef_i = (coef(fit_glmnet_cv, s = "lambda.1se"))@i
  labs = labels(coef(fit_glmnet_cv, s = "lambda.1se"))[[1]]
  labs = labs[-1] # remove intercept
  glmnet_retained = labs[coef_i]
  
  start_form = as.formula(paste("~ ", paste(glmnet_retained , collapse= "+")))
  m = km(start_form, design=X, response=y, nugget=nugget, parinit=parinit,
         nugget.estim=nuggetEstim, noise.var=noiseVar, control=control_list)
  
  return(list(x=X, y=y, nugget=nugget, nuggetEstim=nuggetEstim,
              noiseVar=noiseVar, emulator=m, seed=seed, coefs=m@covariance@range.val,
              trends=m@trend.coef, meanTerms=all.vars(start_form), fit_glmnet_cv=fit_glmnet_cv))
}

twoStep_sens <- function(X, y, n=21, predtype = 'UK', nugget=NULL, nuggetEstim=FALSE, noiseVar=NULL, seed=NULL, trace=FALSE, maxit=100,
                        REPORT=10, factr=1e7, pgtol=0.0, parinit=NULL, popsize=100){
  # Sensitivity analysis with twoStep emulator. 
  # Calculates the variance of the output varied one at a time across each input.
  d = ncol(X)
  X_norm <- normalize(X)
  X_oaat <- oaat_design(X_norm, n, med = TRUE)
  colnames(X_oaat) = colnames(X)
  
  twoStep_em = twoStep_glmnet(X=X, y=y, nugget=nugget, nuggetEstim=nuggetEstim, noiseVar=noiseVar,
                              seed=seed, trace=trace, maxit=maxit,
                              REPORT=REPORT, factr=factr, pgtol=pgtol,
                              parinit=parinit, popsize=popsize)
  
  oaat_pred = predict(twoStep_em$emulator, newdata = X_oaat, type = predtype)
  
  sens = sensvar(oaat_pred = oaat_pred, n=n, d=d)
  out = sens
  out
}

if (file.exists("oat_twostep.rdata")) {
  load("oat_twostep.rdata")
} else {
oat_test <- twoStep_sens(X = X_level1, y = y_level1)


save(oat_test, file = "oat_twostep.rdata")
}

y_names_sum <- c('nbp_lnd_sum', 'fLuc_lnd_sum', 'npp_nlim_lnd_sum', 'cSoil_lnd_sum',
            'cVeg_lnd_sum', 'landCoverFrac_lnd_sum', 'fHarvest_lnd_sum',
            'lai_lnd_sum', 'rh_lnd_sum', 'treeFrac_lnd_sum', 'c3PftFrac_lnd_sum', 
            'c4PftFrac_lnd_sum', 'shrubFrac_lnd_sum', 'baresoilFrac_lnd_sum')




if (file.exists("oaat_Y.rdata")) {
  load("oaat_Y.rdata")
} else {
  
  
oat_var_sensmat_Y <- matrix(NA, nrow = length(y_names_sum), ncol = ncol(X_level1))

for(i in 1:length(y_names_sum)){
  
  yname <- y_names_sum[i]
  y <- Y_level1[, yname]
  oat <- twoStep_sens(X = X_level1, y = y)
  oat_var_sensmat_Y[i, ] <- oat
}

save(y_names_sum, oat_var_sensmat_Y, file = "oaat_Y.rdata")
}

Initial sensitivity Matrix

It looks as though bwl_io is very influential across a number of variables, even though it didn’t appear that interesting in the parginal plots. Why is that?

# normalize the sensitivity matrix
colnames(oat_var_sensmat_Y) <- colnames(X_level1)
rownames(oat_var_sensmat_Y) <- y_names_sum

#test <- normalize(t(oat.var.sensmat))

#image(test)
#par()
heatmap(oat_var_sensmat_Y, Rowv = NA, Colv = NA, mar = c(10,10), scale = 'row')

heatmap(oat_var_sensmat_Y, mar = c(10,10), scale = 'row')

normsens_Y <- normalize(t(oat_var_sensmat_Y))

par(mar = c(12,12,5,2))
image(normsens_Y, axes = FALSE, col = blues)
axis(1, at = seq(from = 0, to = 1, length.out = p), labels = colnames(X_level1), las = 2)
axis(2, at = seq(from = 0, to = 1, length.out = length(y_names_sum)), labels = y_names_sum, las = 1)
mtext('One-at-a-time sensitivity, variance across level 1 ensemble', side = 3, adj = 0, line = 2, cex = 1.8)

Re-examine bwl_io

A closer look at bwl_io now that the impact of f0_io has been removed shows a large number of “zero” NPP when bwl_io is at low values, which could well be the source of apparent sensitivity.

Take only higher values of bwl_io for the next round of constraints.

p <- ncol(X_level1)

y_level1 <- Y_level1[,'npp_nlim_lnd_sum']

par(mfrow = c(5,7), mar = c(3,1,3,1))
for(i in 1:p){
  plot(X_level1[,i], y_level1, xlab = '', ylab = '', main = colnames(X_level1)[i])
}

# This fails for "cVeg_lnd_sum"
# The result will be that some of the columns are repeated.

if (file.exists("oaat_YAnom.rdata")) {
  load("oaat_YAnom.rdata")
} else {

oat_var_sensmat_YAnom <- matrix(NA, nrow = length(y_names_sum), ncol = ncol(X_level1))

for(i in 1:length(y_names_sum)){
  
  yname <- y_names_sum[i]
  y <- YAnom_level1[, yname]
  try(oat <- twoStep_sens(X = X_level1, y = y))
  oat_var_sensmat_YAnom[i, ] <- oat
}

save(y_names_sum, oat_var_sensmat_YAnom, file = "oaat_YAnom.rdata")

}

# normalize the sensitivity matrix
colnames(oat_var_sensmat_YAnom) <- colnames(X_level1)
rownames(oat_var_sensmat_YAnom) <- y_names_sum

#test <- normalize(t(oat.var.sensmat))

#image(test)
#par()
heatmap(oat_var_sensmat_YAnom, Rowv = NA, Colv = NA, mar = c(10,10), scale = 'row')

heatmap(oat_var_sensmat_YAnom, mar = c(10,6), scale = 'row')

normsens_YAnom <- normalize(t(oat_var_sensmat_YAnom))

par(mar = c(12,12,5,2))
image(normsens_YAnom, axes = FALSE, col = blues)
axis(1, at = seq(from = 0, to = 1, length.out = p), labels = colnames(X_level1), las = 2)
axis(2, at = seq(from = 0, to = 1, length.out = length(y_names_sum)), labels = y_names_sum, las = 1)
mtext('One-at-a-time sensitivity, variance of historical change across level 1 ensemble', side = 3, adj = 0, line = 2, cex = 1.8)

Plot both sensitivity matrices on top of one another.

It looks as though both the absolute value and the change over time are controlled by the same parameters.

par(mfrow = c(2,1), mar = c(12,12,5,2))

image(normsens_Y, axes = FALSE, col = blues)
axis(1, at = seq(from = 0, to = 1, length.out = p), labels = colnames(X_level1), las = 2)
axis(2, at = seq(from = 0, to = 1, length.out = length(y_names_sum)), labels = y_names_sum, las = 1)
mtext('One-at-a-time sensitivity, variance of historical change across level 1 ensemble', side = 3, adj = 0, line = 2, cex = 1.8)


image(normsens_YAnom, axes = FALSE, col = blues)
axis(1, at = seq(from = 0, to = 1, length.out = p), labels = colnames(X_level1), las = 2)
axis(2, at = seq(from = 0, to = 1, length.out = length(y_names_sum)), labels = y_names_sum, las = 1)
mtext('One-at-a-time sensitivity, variance of historical change across level 1 ensemble', side = 3, adj = 0, line = 2, cex = 1.8)

How good are the emulators for each output?

The emulators appear to be at least capturing the broad response for all of the output variables.

First, plot the straight kriging emulators

if (file.exists("km_emulators_Y.rdata")) {
  load("km_emulators_Y.rdata")
} else {
  
  emlist_km_Y <- vector(mode = 'list', length = length(y_names_sum))
  
  for(i in 1:length(y_names_sum)){
    yname <- y_names_sum[i]
    y <- Y_level1[, yname]
    
    em <- km(~., design = X_level1, response = y)
    emlist_km_Y[[i]] <- em
  }
  
  loolist_km_Y <- vector(mode = 'list', length = length(y_names_sum))
  
  for(i in 1:length(y_names_sum)){
    
    loo <- leaveOneOut.km(model = emlist_km_Y[[i]], type = 'UK', trend.reestim = TRUE)
    loolist_km_Y[[i]] <- loo
  }
  
  save(emlist_km_Y,loolist_km_Y, file = "km_emulators_Y.rdata")
}

par(mfrow = c(4,4), mar = c(3,4,2,2), oma = c(4,4,4,0.1))
for(i in 1:length(loolist_km_Y)){
  
  y <- Y_level1[, y_names_sum[i]]
  loo <- loolist_km_Y[[i]]
  ylim <- range(c(loo$mean - (2*loo$sd), loo$mean + (2*loo$sd)) )
  plot(y, loo$mean, xlab = '', ylab = '', main = colnames(Y_level1)[i] , ylim = ylim, col = makeTransparent('black', 70),
       pch = 19)
  segments(x0 = y, y0 = loo$mean - (2*loo$sd)  , x1 = y , y1 = loo$mean + (2*loo$sd), col = makeTransparent('black', 70))
  abline(0,1)

}

mtext('Actual', side = 1, line = 1, outer = TRUE, cex = 2 )
mtext('Predicted', side = 2, line = 0, outer = TRUE, cex = 2) 
mtext('Modern Value (Y)', side = 3, line = 0, outer = TRUE, cex = 2) 

if (file.exists("km_emulators_YAnom.rdata")) {
  load("km_emulators_YAnom.rdata")
} else {
  
  emlist_km_YAnom <- vector(mode = 'list', length = length(y_names_sum))
  
  for(i in 1:length(y_names_sum)){
    yname <- y_names_sum[i]
    y <- YAnom_level1[, yname]
    
    em <- km(~., design = X_level1, response = y)
    emlist_km_YAnom[[i]] <- em
  }
  
  loolist_km_YAnom <- vector(mode = 'list', length = length(y_names_sum))
  
  for(i in 1:length(y_names_sum)){
    
    loo <- leaveOneOut.km(model = emlist_km_YAnom[[i]], type = 'UK', trend.reestim = TRUE)
    loolist_km_YAnom[[i]] <- loo
  }
  
  save(emlist_km_YAnom,loolist_km_YAnom, file = "km_emulators_YAnom.rdata")
}

km emulators for change in variables over time

par(mfrow = c(4,4), mar = c(3,4,2,2), oma = c(4,4,4,0.1))
for(i in 1:length(loolist_km_YAnom)){
  
  y <- YAnom_level1[, y_names_sum[i]]
  loo <- loolist_km_YAnom[[i]]
  ylim <- range(c(loo$mean - (2*loo$sd), loo$mean + (2*loo$sd)) )
  plot(y, loo$mean, xlab = '', ylab = '', main = colnames(YAnom_level1)[i] , ylim = ylim, col = makeTransparent('black', 70),
       pch = 19)
  segments(x0 = y, y0 = loo$mean - (2*loo$sd)  , x1 = y , y1 = loo$mean + (2*loo$sd), col = makeTransparent('black', 70))
  abline(0,1)

}

mtext('Actual', side = 1, line = 1, outer = TRUE, cex = 2 )
mtext('Predicted', side = 2, line = 0, outer = TRUE, cex = 2) 
mtext('Change over time (YAnom)', side = 3, line = 1, outer = TRUE, cex = 2) 

Next, plot the twostep glmnet/km emulators

# Twostep glmnet emulators

if (file.exists("ts_emulators_Y.rdata")) {
  load("ts_emulators_Y.rdata")
} else {
  
  emlist_twoStep_glmnet_Y <- vector(mode = 'list', length = length(y_names_sum))
  
  for(i in 1:length(y_names_sum)){
    
    yname <- y_names_sum[i]
    y <- Y_level1[, yname]
    
    em <- twoStep_glmnet(X = X_level1, y = y)
    emlist_twoStep_glmnet_Y[[i]] <- em
  }
  
  loolist_twoStep_glmnet_Y <- vector(mode = 'list', length = length(y_names_sum))
  
  for(i in 1:length(y_names_sum)){
    
    loo <- leaveOneOut.km(model = emlist_twoStep_glmnet_Y[[i]]$emulator, type = 'UK', trend.reestim = TRUE)
    loolist_twoStep_glmnet_Y[[i]] <- loo
  }
  
  save(emlist_twoStep_glmnet_Y, loolist_twoStep_glmnet_Y, file = "ts_emulators_Y.rdata")

}

TwoStep emulator performance for modern values

par(mfrow = c(4,4), mar = c(3,4,2,2), oma = c(4,4,4,0.1))
for(i in 1:length(loolist_twoStep_glmnet_Y)){
  
  y <- Y_level1[, y_names_sum[i]]
  loo <- loolist_twoStep_glmnet_Y[[i]]
  ylim <- range(c(loo$mean - (2*loo$sd), loo$mean + (2*loo$sd)) )
  plot(y, loo$mean, xlab = '', ylab = '', main = colnames(Y_level1)[i] , ylim = ylim, col = makeTransparent('black', 70),
       pch = 19)
  segments(x0 = y, y0 = loo$mean - (2*loo$sd)  , x1 = y , y1 = loo$mean + (2*loo$sd), col = makeTransparent('black', 70))
  abline(0,1)

}

mtext('Actual', side = 1, line = 1, outer = TRUE, cex = 2 )
mtext('Predicted', side = 2, line = 0, outer = TRUE, cex = 2) 
mtext('Modern Value (Y)', side = 3, line = 0, outer = TRUE, cex = 2) 

# Write an emulator wrapper

# Write a leave-one-out wrapper

# Create a list of emulator fits, for both km and twoStep methods.
# Use mclapply to build the lists
# use code from HDE package
# Make sure errors are handled adequately.


# Can we write it to use any emulator? (i.e km, twostep, something from another package?)

Direct twoStep emulator using foreach

library(doParallel)
registerDoParallel(cores = detectCores() - 1)

direct_twoStep_glmnet_parallel <- function(X, Y, ...){
  
  d <- ncol(Y)
  
  out <- vector(mode='list', length=d)
  
  foreach(i = 1:d) %dopar% {
    
    y <- Y[,i]
    
    em <- twoStep_glmnet(X=X, y = y, ...)
    out[i] <- em
 
  }
  
  out
} 

# I actually wrote code to do this createKmFitList, which isn't parallel at the moment.
# Maybe make it parallel in the next version?

library(doParallel)
registerDoParallel(cores = detectCores() - 1)

direct_twoStep_glmnet_parallel <- function(X, Y, ...){
  
  d <- ncol(Y)
  foreach(i = 1:d) %dopar% {
    
    y <- Y[,i]
    
    em <- twoStep_glmnet(X=X, y = y, ...)
  }
} 

History matching and generation of new ensemble members

# In order to use the history matching code, we'll need to specify targets -
# specifically "observations" with uncertainty that approximately match our
# "hard boundaries" from the existing constraints.

# Initial guess just choose the centre of the (implied) uniform distribution.
#cs_gb.target = (3000 - 750) / 2
#cv.target = (800 - 300) / 2
#npp_n_gb.target = (80 - 35) / 2
#runoff.target = 1
#nbp.target = 0
#gpp.target = 75

#Y.target = c(cs_gb.target, cv.target, npp_n_gb.target, runoff.target, nbp.target)

ynames_const <- c('nbp_lnd_sum', 'npp_nlim_lnd_sum', 'cSoil_lnd_sum', 'cVeg_lnd_sum')
yunits_const <- c('GtC/year', 'GtC/year', 'GtC', 'GtC')
Y_const_level1 <- Y_level1[, ynames_const]

scalevec <- c(1e12/ysec, 1e12/ysec, 1e12, 1e12)
Y_const_level1_scaled <- sweep(Y_const_level1,2, STATS = scalevec, FUN = '/' )


years = 1861:2014
ysec = 60*60*24*365
# This is a "normalisation vector", for making the output numbers more manageable.
#cs_gb       cv    gpp_gb        nbp npp_n_gb    runoff
norm_vec = c(1e12, 1e12, 1e12/ysec , 1e12, 1e12, 1e9)

# nbp  npp  csoil  cveg
Y_lower <- c(-10, 35, 750, 300)
Y_upper <- c(10, 80, 3000, 800)

# I'm going to set it so that +3sd aligns approximately with the original limits
# given by Andy Wiltshire.
Y_target = (Y_upper - abs(Y_lower)) / 2 # abs() to fix the problem with negative numbers


# standard deviation is derived from the limits and the central target
# (this distance is assumed to be 3 standard deviations.
Y_sd = (Y_upper - Y_target) / 3
names(Y_sd) = colnames(Y_const_level1_scaled)


p = ncol(Y_const_level1_scaled)

obs_sd_list = as.list(rep(0.01,p))
disc_list =  as.list(rep(0,p)) 
disc_sd_list =  as.list(Y_sd/2)
thres = 3

mins_aug = apply(X_level1, 2, FUN = min)
maxes_aug =apply(X_level1, 2, FUN = max)

# convert Y_target for ingestion into function
Y_target = matrix(Y_target, nrow = 1)

Augment the design.

The function addNroyDesignPoints builds an emulator for each model output in Y. It compares the output of each emulator at a number of candidate desin points, and chooses a space-filling set of them that that are Not Ruled Out Yet (statistically close to the observation at Y_target).

# Final output needs to be expressed in terms of original LHS, then put back out to conf files.

# This function adds n.aug potential design points, and finds their implausibility
# score in X.nroy

wave1 = addNroyDesignPoints(X = X_level1, 
                            Y = Y_const_level1_scaled, 
                            Y_target = Y_target,
                            n_aug = 10000, 
                            mins_aug = mins_aug,
                            maxes_aug = maxes_aug,
                            thres = 3,
                            disc_list=disc_list,
                            disc_sd_list = disc_sd_list,
                            obs_sd_list = obs_sd_list,
                            n_app = 50,
                            nreps = 100)

Write the augmented design

The function write_jules_design here simply takes the points calculated by addNroyDesignPoints and writes them to configuration files.

# this needs sorting
source('~/myRpackages/julesR/vignettes/default_jules_parameter_perturbations.R')

# Easiest way to generate a design of the right size is to have a "fac" which takes
# the names from the parameter list, and then multiplies everything by 0.5 or 2

tf <- 'l_vg_soil'
# we don't want anything that is TRUE/FALSE to be in fac
fac_init <- names(paramlist)
not_tf_ix <- which(names(paramlist)!=tf)
paramlist_trunc <-paramlist[not_tf_ix]

fac <- names(paramlist_trunc)

maxfac <-lapply(paramlist_trunc,function(x) x$max[which.max(x$max)] / x$standard[which.max(x$max)])
minfac <- lapply(paramlist_trunc,function(x) x$min[which.max(x$max)] / x$standard[which.max(x$max)])

# create a directory for the configuration files
confdir <- 'conf_files_augment_JULES-ES-1p0'

dir.create(confdir)

## Warning in dir.create(confdir): 'conf_files_augment_JULES-ES-1p0' already
## exists

X_mm <- wave1$X_mm

# This is the function that writes the configuration files.
write_jules_design(X_mm = X_mm, paramlist=paramlist, n = nrow(X_mm),
                    fac = fac, minfac = minfac, maxfac = maxfac,
                    tf = tf,
                    fnprefix = paste0(confdir,'/param-perturb-P'),
                    lhsfn = paste0(confdir,'/lhs_example.txt'),
                    stanfn = paste0(confdir,'/stanparms_example.txt'),
                    allstanfn = paste0(confdir,'/allstanparms_example.txt'),
                    rn = 12,
                    startnum = 500)

Check the design

Check that the augmented design produces what we expect. New ensemble members should be somewhat constrained within the boundaries of the original design, if the comparison to data offers any constraint.

X_mm <- wave1$X_mm

pairs(rbind(X, X_mm), xlim = c(0,1), ylim = c(0,1), gap = 0, lower.panel = NULL, 
      col = c(rep('grey', nrow(X)), rep('red', nrow(X_mm))),
      pch = c(rep(21, nrow(X)), rep(20, nrow(X_mm)))
      )

par(xpd = NA)

legend('bottom',
       legend = c('Original design', 'New points'),
       col = c('grey', 'red'),
       inset = 0.15,
       cex = 1.5,
       pch = c(21,20)
)

# with 3 processers, using foreach parallel processing takes approximately 1/3 the time (around 20 seconds per emulator) of looping the emulator fitting directly. I'd hope this would scale with processor numbers - it'll be worth trying on SPICE.

# system.time(testloop_par <- direct_twoStep_glmnet_parallel(X=X_level1, Y = Y_level1))

direct_twoStep_glmnet <- function(X, Y, ...){
  
  d <- ncol(Y)
  
  out <- vector(mode='list', length=d)
  
  for(i in 1:d){
    
    y <- Y[,i]
    
    em <- twoStep_glmnet(X=X, y = y, ...)
    out[i] <- em
 
  }
  
  out
} 

# system.time(testloop <- direct_twoStep_glmnet(X=X_level1, Y_level1))

# Test parallel processing against a foreach processing (and maybe mclapply?)

#system.time(testloop_par <- direct_twoStep_glmnet_parallel(X=X_level1, Y_level1))

emList <- function(X, Y){
  # Create a list of objects to be emulated
  # X             design matrix with (nrow) instances of (ncol) inputs
  # Y             matrix of outputs, with one row
  #               for each row of X

  d <- ncol(Y)
  em_list <- vector(mode='list', length=d)

  for(i in 1:d){
    em_obj <- NULL
    em_obj$X <- X
    em_obj$y <- Y[, i]
    em_list[[i]] <- em_obj
  }
  em_list
}

#test <- emlist(X_level1, Y_level1)

#mclapply(X = test, FUN = km)

# function from hde for direct prediction
direct.pred = function (form, X, Y, Xnew, ...){
  # Directly applies km in parallel to predict each column of an ensemble
  ens.list = emlist(X = X, Y = Y)
  km.list = mclapply(ens.list, FUN = km.wrap, form = form)

  pred.list = mclapply(km.list, FUN = km.pred.wrap, Xnew = as.matrix(Xnew, nrow = 1), type = "UK")

  out.mean = sapply(pred.list, FUN=extract.predmean)
  out.sd = sapply(pred.list, FUN=extract.predsd)
  return(list(mean = out.mean, sd = out.sd))
}